Rafter last month banned Tomic from next month's Davis Cup tie in Taiwan because of attitude problems.
Seemingly in retaliation, the 20-year-old says he will also skip Australia's subsequent tie in April and possibly return for a World Group playoff in September.
With Rafter employed by TA to handle Davis Cup matters, TA's off-court administration says it will be left to the captain to deal with Tomic how he he sees fit, without any interference from above.
"It's Pat's call. He's the Davis Cup captain, he handles the Davis Cup team and that's really up to him to handle," TA chief executive Steve Wood said on Thursday.
"Pat and the team work together. It's really for Pat to handle. That's the key behind how we run the team.
"Pat and Bernard will work that out and we're just looking forward to a great Australian Open and getting some wins on the board for Bernard and the rest of the Australians."
Australia's long-time Davis Cup stalwart Lleyton Hewitt has also expressed his concerns over Tomic not making himself available for the April tie.
Rafter has taken a tough love approach to Tomic, publicly slamming the Gold Coast youngster when he performed poorly against Andy Roddick at last year's US Open.
But Tomic has started the Australian summer having turned around his form markedly, renewing hopes he could go deep into next week's Australian Open.
Meanwhile, Korean motor car company Kia has renewed its major sponsorship of the Australian Open for the next five years.
The multi-million-dollar deal will continue until at least the 2018 Open.